Contacts of the strand formed by residues 73 - 78 (chain J) in PDB entry 1VCB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 73 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4J PHE 2.8 6.9 + - - -
5J LEU* 3.3 12.1 - - + +
6J MET* 2.8 26.8 + - - +
62J PHE* 3.6 31.4 - - + -
66J THR* 3.8 23.3 - - + +
67J ALA* 3.8 6.9 - - + +
71J ALA 3.8 1.0 + - - -
72J PRO* 1.3 72.5 - - - +
74J THR* 1.3 61.2 + - - +
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Residues in contact with THR 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J MET* 3.4 32.5 - - - +
8J ARG* 3.9 25.3 + - + +
45J TYR 4.5 1.9 - - - +
46J LYS* 4.8 7.6 - - - +
47J ASP* 5.4 2.6 + - - +
62J PHE* 4.0 9.5 - - - -
72J PRO 3.9 1.4 + - - -
73J ALA* 1.3 72.7 - - - +
75J VAL* 1.3 72.6 + - - +
76J GLY 4.3 1.2 + - - +
90J ILE* 4.7 10.3 - - + -
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Residues in contact with VAL 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J LEU* 4.3 24.7 - - + -
6J MET 3.1 6.5 + - - -
7J ILE* 3.4 14.9 - - + +
8J ARG* 2.6 33.8 + - - +
27J LEU* 4.6 8.1 - - + -
44J LEU* 4.1 25.4 - - + -
45J TYR 3.4 12.8 - - - +
51J LEU* 4.8 3.1 - - + -
62J PHE* 3.6 31.6 - - + -
74J THR* 1.3 77.2 - - - +
76J GLY* 1.3 71.9 + - - +
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Residues in contact with GLY 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J ARG 3.5 5.6 - - - -
44J LEU* 3.3 8.3 - - - +
45J TYR* 2.9 40.0 + - - -
46J LYS* 5.1 0.6 - - - +
47J ASP 5.6 1.0 - - - +
74J THR* 4.2 2.0 - - - +
75J VAL* 1.3 79.0 - - - +
77J LEU* 1.3 59.4 + - - -
88J LEU* 3.8 16.8 - - - -
90J ILE* 4.1 9.6 - - - -
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Residues in contact with LEU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ILE* 4.3 15.7 - - + +
8J ARG 2.9 10.3 + - - +
9J ARG* 3.4 38.6 - - + +
14J ILE* 5.9 0.2 - - + -
31J VAL* 4.0 8.7 - - + -
35J LEU* 3.8 29.2 - - + -
42J GLN* 3.7 27.4 - - + +
43J ARG 3.4 6.3 - - - +
44J LEU* 3.3 23.6 - - + -
45J TYR* 4.8 0.2 - - - -
76J GLY* 1.3 75.1 - - - +
78J ALA* 1.3 66.4 + - - +
79J PHE* 3.9 12.8 - - + -
86J GLU* 4.5 0.7 - - - +
88J LEU* 3.2 17.1 - - - +
89J CYS 4.8 1.4 + - - -
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Residues in contact with ALA 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG* 4.6 0.2 - - - +
41J GLU 3.8 0.2 - - - +
42J GLN* 3.4 5.7 - - - +
43J ARG* 3.0 37.0 + - + +
45J TYR* 3.7 26.5 - - + +
77J LEU* 1.3 76.6 - - - +
79J PHE* 1.3 63.9 - - - +
85J PHE* 5.5 0.6 - - + +
86J GLU* 3.8 28.7 - - + +
88J LEU* 4.5 8.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il